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16.4: Regulating Gene Expression in Cell Development - Biology

16.4: Regulating Gene Expression in Cell Development - Biology


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16.4: Regulating Gene Expression in Cell Development

Chapter Summary

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is mostly regulated at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.

16.2 Prokaryotic Gene Regulation

The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by the trp operon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last example—the lac operon—two conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for the lac operon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription.

16.3 Eukaryotic Epigenetic Gene Regulation

In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.

16.4 Eukaryotic Transcriptional Gene Regulation

To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.

16.5 Eukaryotic Post-transcriptional Gene Regulation

Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly however, miRNAs always decrease stability and promote decay.

16.6 Eukaryotic Translational and Post-translational Gene Regulation

Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein.

16.7 Cancer and Gene Regulation

Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer.


16.1Regulation of Gene Expression While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the enti .

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This text is based on Openstax Biology for AP Courses, Senior Contributing Authors Julianne Zedalis, The Bishop's School in La Jolla, CA, John Eggebrecht, Cornell University Contributing Authors Yael Avissar, Rhode Island College, Jung Choi, Georgia Institute of Technology, Jean DeSaix, University of North Carolina at Chapel Hill, Vladimir Jurukovski, Suffolk County Community College, Connie Rye, East Mississippi Community College, Robert Wise, University of Wisconsin, Oshkosh

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 Unported License, with no additional restrictions


16 Gene Regulation

Most people know that regular exercise is important to maintain good health. It promotes cardiovascular health and helps to prevent obesity. Scientists have now discovered that long-term endurance training also changes how genes are expressed in muscle tissue. In a recent study, 23 healthy people each exercised one leg for 45 minutes four days a week while resting the other leg. After three months, muscles from participants’ legs were biopsied, and scientists analyzed the activity level of over 20,000 genes in the tissue samples.

They found that for each participant the exercised leg had reduced inflammation and improved metabolism compared with the non-exercised leg. These differences were accompanied by changes in genes associated with metabolism and inflammation. However, the actual nucleotide sequences of the genes weren’t changed. Instead, some genes were methylated, which simply means methyl groups were attached to certain nucleotides along the sequence. This, essentially, turned the genes “off” or otherwise changed how they were expressed. DNA methylation is an example of epigenetics, which is a process that alters genes without affecting the nucleotide sequence of the genes. The full research article can be found here.

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This text is based on Openstax Biology for AP Courses, Senior Contributing Authors Julianne Zedalis, The Bishop's School in La Jolla, CA, John Eggebrecht, Cornell University Contributing Authors Yael Avissar, Rhode Island College, Jung Choi, Georgia Institute of Technology, Jean DeSaix, University of North Carolina at Chapel Hill, Vladimir Jurukovski, Suffolk County Community College, Connie Rye, East Mississippi Community College, Robert Wise, University of Wisconsin, Oshkosh

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 Unported License, with no additional restrictions


16.4: Regulating Gene Expression in Cell Development - Biology

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is mostly regulated at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.

16.2 Prokaryotic Gene Regulation

The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by the trp operon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last example—the lac operon—two conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for the lac operon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription.

16.3 Eukaryotic Epigenetic Gene Regulation

In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.

16.4 Eukaryotic Transcriptional Gene Regulation

To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.

16.5 Eukaryotic Post-transcriptional Gene Regulation

Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly however, miRNAs always decrease stability and promote decay.

16.6 Eukaryotic Translational and Post-translational Gene Regulation

Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein.

16.7 Cancer and Gene Regulation

Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer.

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This text is based on Openstax Biology for AP Courses, Senior Contributing Authors Julianne Zedalis, The Bishop's School in La Jolla, CA, John Eggebrecht, Cornell University Contributing Authors Yael Avissar, Rhode Island College, Jung Choi, Georgia Institute of Technology, Jean DeSaix, University of North Carolina at Chapel Hill, Vladimir Jurukovski, Suffolk County Community College, Connie Rye, East Mississippi Community College, Robert Wise, University of Wisconsin, Oshkosh

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 Unported License, with no additional restrictions


Regulation of Gene Expression in Eukaryotes | Gene Regulation

The variation in the rate of transcription often regulates gene expression. Interactions between RNA polymerase II and basal trans­cription factors leading to the formation of the transcription initiation complex influence the rate of transcription. Other transcription factors change the rate of transcription initiation by binding to promoter sequences. The rate of transcription is also influenced by enhancers and silencers.

This is a site for regulation of transcription. Every structural gene in eukaryotes has the promoter site which consists of several hundred nucleotide sequences that serve as the recognition point for RNA polymerase binding, located at a fixed distance from the site where transcription is initiated.

Eukaryotic pro­moters require the binding of a number of protein factors to initiate transcription. Promoter regions are recognized by RNA polymerase II, which transcribes primarily mRNA, consists of short DNA sequences usually located within 100 bp upstream (in the 5′ direction) of the gene.

The promoter regions of most eukaryotic gene contain several specific regions such as:

Variation in the rate of transcrip­tion often regulates gene expression. Interactions between RNA polymerase II and basal transcrip­tion factors lead to formation of transcription initiation complex (TIC) at the TATA box.

It is located about 25-30 bases upstream from the initial point of transcription, it consists of an 8 bp consensus sequence composed of A = T base pairs (TATAAA) only, but flanked on either side by G=C rich regions. Mutation in TATA box reduces transcription or may alter the initiation point. TATA box is also known as Hogness box.

Many promoters contain other components and also bear the consensus sequence like GGCCAATC which is situated at the region 70-80 bp from the start site, it can function in both 5-3′ or a 3-5′ orientation. Mutational analysis showed that CAAT box plays the strongest role in determining the efficiency of the promoter.

Another element often seen in some promoter regions, called the GC box, has the consensus sequence GGGCGG and is found at about position -110, often occurs in multiple copies, the GC elements bind transcription fac­tors and function more like enhancer.

Binding of RNA Polymerase II to Promoters:

The binding of RNA polymerase II to its promo­ter site requires a number of transcriptional factors (TPs).

Promoters have multiple binding sites for transcription factors each of which can influence transcription. TF IID is the first transcriptional factor to bind close to the promoter at an initiator site about -20 to -10 base pairs before the transcrip­tional start site, i.e., at the TATA boxes, so it is also called TATA box binding protein (TBP).

TF IID may also interact with other transcriptional factors like TF IIA, TF MB and TF ME. A complex consisting of all transcriptional factors determine which RNA polymerase binds and which gene can be transcribed, and the complex is called pre-initiation complex.

The transcription factors have a modular structure containing DNA binding, dimerization and transactivation domains.

DNA binding domains contain three motifs: helix-turn-helix, zinc fingers and basic domains which occur in combination with dimerization domains.

Dimeri­zation domains contain two motifs: leucine zippers and helix-loop-helix.

Dimerization allows the formation of homo- and heterodimers creating transcription factors with diverse func­tions. Transactivation domains have no motifs but are often enriched with acidic amino acid, glutamines or pro-lines. They interact with a variety of proteins at different stages during trans­cription. Transcription factors can also repress transcription by direct or indirect mechanisms.

The transcriptional factors are produced constitutively, but except these there are some transcriptional activators (TAs) which bind to the enhancer site situated many hundreds base pairs from the promoter site.

These transcriptional activators are induced proteins, i.e., synthesized only in response to specific signals, which on binding with DNA forms the loop back on itself when they interact with the TFs near the promoter. This interaction between enhancer site and initiation site is usually necessary for transcription above a basal level (Fig. 17.10).

Co-activators are activator proteins that often connect TFs and TAs and may be essential for expression of gene at high level.

There are many ways by which negative control of transcription takes place in eukaryotes.

These can be divided into 3 main categories:

(1) Inhibition of DNA binding

(ii) Blocking of activation

(iii) Silencing, i.e., transcriptional activation factor (TAP) cannot bind with transcrip­tion initiation complex (TIC) due to pre­sence of silencer factor.

Like an enhancer, a silencer also functions irrespective of its position (many thousands base pairs away) and orientation relative to the gene, whose expression it controls. The silencer factor (a protein) either locks the transcription initiation complex or makes it unavailable for activating factors or it disorganizes the transcription initia­tion complex (Fig. 17.11).

Among the various models, the Britten and Davidson model for regulation of protein synthesis in eukaryotes is most popular. This model is also called genes controlled by one sensor site is termed as battery.

This model assumes the presence of four classes of sequences (Fig. 17.12a):

It is comparable with the structural gene of a prokaryotic operon.

It is comparable to operator gene in bacterial operon and one such receptor site is always assumed to be present adjacent to each producer gene or a set of producer gene.

It is comparable to regu­lator gene and is responsible for synthesis of an activator RNA that may or may not give rise to proteins before it activates the receptor site.

A sensor site regulates the activity of integrator gene, which can be transcribed only when the sensor site is activated by agents like hormones and proteins, changes the pattern of gene expression. In this model the genes (producer gene and integrator gene) are involved in RNA synthesis whereas receptor and sensor sites are those sequences which help only in recognition with­out taking part in RNA synthesis.

It is proposed in this model that receptor sites and integrator genes may be repeated a number of times to control the activity of a large number of genes in the same cell. Repetition of receptor ensures that same activator recognises all of them and several enzymes of one pathway are simultaneously synthesized.

When the transcription of same gene is needed at different developmental stages, it can be achieved by multiplicity of receptor sites and integrator genes.

Each producer gene may have several recep­tor sites, each responding to one activator (Fig. 17.12b) so that a single activator thus can recog­nize several genes at a time. One sensor site may regulate the activity of several integrators and different activators may activate the same gene at different times. An inte­grator gene may also fall in cluster with same sensor site (Fig. 17.12c).

Regulation of Gene Expression by Hor­mones:

Hormones influence target cells by activating gene transcription. Steroid hormones on entering cells, bind steroid hormone recep­tor protein, releasing it from an inhibitory pro­tein. The receptor dimerizes and is trans-located to the nucleus where it binds to target gene promoters activating transcription.

Polypeptide hormones bind receptor proteins on the surface of target cells. Signal transduction triggers gene activation in which a sequential activation of several proteins by phosphorylation takes place.

Post-Transcriptional Regulation of Gene Expression in Eukaryotes:

Post-transcriptional regulation of gene expression may occur in different ways.

Regulation of Processing:

Post-transcriptional modes of regulation also occur in many organisms where the eukaryotic nuclear RNA transcripts are modified prior to translation, non-coding introns are removed, the remaining exons are precisely spliced together and the mRNA is modified by the addition of cap at the 5′ end and a poly-A tail after end.

The message is then complexed with proteins and exported to the cytoplasm. Each of these pro­cessing steps offers several possibilities for regulation, for example, several alternative splicing pathways of a single pre-mRNA trans­cript to give multiple mRNAs and regulation of the stability of mRNA itself. This leads to the synthesis of different proteins or isoforms in the same time and space.

Regulation of Translation:

Regulation at translational level occurs in different ways:

(i) Activation and repression of translation:

In eukaryotes the activator protein binds to mRNA and leads to the formation of hairpin structure which helps in ribosome binding with mRNA by the exposure of 5′ end. The translational repressor protein (IRE-BP) controls ferritin synthesis by down-regulation and transferring receptor synthesis by up-regulation.

(ii) Regulation by phosphorylation machi­nery:

Translational repressor protein may regulate the translation in eukaryotic system or regulation of translation is brought about by modification of general components of translational machinery.

Reversible phosphorylation machinery is involved in the regulation of gene expres­sion, as the phosphorylated or dephosphorylated forms of the components of translational machinery should identify a specific mRNA from the bulk mRNA population.


Regulation of Gene Expression: Negative and Positive Regulation

The two types of gene expression regulation are: (1) Negative Regulation and (2) Positive Regulation. And also discuss about some important terms used in connection with the regulation of gene expression.

Most of the genes of an organism produce specific proteins (enzymes), which, in turn produce specific phenotypes. The genes whose mRNA transcripts are translated into protein are known as structural genes. Every cell of an organism possesses all the structural genes normally present in the species, but only a small fraction of them are functional in any cell at a given time.

In prokaryotes, cells generally synthesize only those enzymes which they need in a given environment. For example, E. coli cells grown in the presence of lactose produce abundant (up to 3000 molecules/cell) β-galactosidase, the enzyme that hydrolyses lactose. However, very little of this enzyme (less than 3 molecules/cell) is produced in the absence of lactose.

In eukaryotes, the cells of different organs produce different proteins needed for their function. Red blood cells contain a high concentration of hemoglobin, while leucocytes (white blood cells) have no hemoglobin at all.

Apparently, there is a precise control on the kinds of proteins or enzymes product in a given tissue or cell at a given time. Such a control on gene activity, i.e., protein production, that permits the function of only those genes whose products are required in a given cell at a given time is termed as gene regulation.

Synthesis of enzyme depends mainly on two factors in a degradative process, the synthesis of enzyme depends on the availability of the molecule to be degraded. If the molecule is in more quantity, the enzyme synthesis will be more and vice versa. In a biosynthetic pathway, the synthesis of an enzyme is controlled by the end product. If the end product is more, the enzyme synthesis will be less and vice versa.

There are two types of gene regulation, viz:

(1) Negative regulation, and

(1) In negative regulation:

An inhibitor is present in the cell/system, that prevents transcription by inactivating the promoter. This inhibitor is known as repressor. For initiation of transcription, an inducer is required. Inducer acts as antagonist of the repressor. In the negative regulation, absence of product increases the enzyme synthesis and presence of the product decreases the synthesis.

(2) In positive regulation:

An effector molecule (which may be a protein or a molecular complex) activates the promoter for transcription. In a degradative system, either negative or positive mechanism may operate, while in a biosynthetic pathway negative mechanism operates (e.g., lac operon).

The phenomenon of gene expression can be elaborated further such as given below:

1. Gene expression is the mechanism at the molecular level by which a gene is able to express itself in the phenotype of an organism.

2. The mechanism of gene expression involves biochemical genetics. It consists of synthesis of specific RNAs, polypeptides, structural proteins, proteinaceous bio-chemicals or enzymes which control the structure or functioning of specific traits.

3. Gene regulation is the mechanism of switching off and switching on of the genes depending upon the requirement of the cells and the state of development.

4. It is because of this regulation that certain proteins are synthesized in as few as 5-10 molecules while others are formed in more than 100,000 molecules per cell.

5. There are two types of gene regulations positive and negative.

6. In negative gene regulation the genes continue expressing their effect till their activity is suppressed.

7. This type of gene regulation is also called repressible regulation.

8. The repression is due to a product of regulatory genes.

9. Positive gene regulation is the one in which the genes remain non-expressed unless and until they are induced to do it.

10. It is, therefore called inducible regulation.

11. Here a product removes d biochemical that keeps the genes in non-expressed state.

12. As the genes express their effect through enzymes, their enzymes are also called inducible enzymes and repressible enzymes.

Gene regulation is exerted at four levels:

1. Transcriptional level when primary transcript is formed.

2. Processing level when splicing and terminal additions are made.

3. Transport of mRNA out of nucleus into cytoplasm.

Important Terms used in Connection with the Regulation of Gene Expression:

In operon, protein molecules which prevent transcription. The process of inhibition of transcription is called repression.

The substance that allows initiation of transcription (e.g., lactose in lac operon). Such process is known as induction.

A combination of repressor and a metabolite which prevents protein synthesis. Such process is known as co-repression.

An enzyme whose production is enhanced by adding the substrate in the culture medium. Such system is called inducible system.

An enzyme whose production can be inhibited by adding an end product. Such system is known as repressible system.

6. Constitutive Enzyme:

An enzyme whose production is constant irrespective of metabolic state of the cell.

Inhibition of transcription by repressor through inactivation of promoter, e.g., in lac operon.

Enhancement of transcription by an effector molecule through activation of pro-motor.


Highlights in European Plant Biotechnology Research and Technology Transfer

Concluding remarks

Only very recently it has become clear that the post-transcriptional events of pre-mRNA processing and RNA decay are important and sensitive control levels in plant gene expression. Plants have to react fast and efficiently to a large number of developmental and environmental factors. Post-transcriptional RNA processing and decay may be the level of tuning gene expression accordingly. The RNA level may also be the level of intra- and intercellular signaling needed for the spatial and temporal synchronization of plant gene expression patterns [ 35 ]. Gene silencing research was able to identify some of the involved candidate molecules because the introduction of foreign genes into plant genomes has disturbed the balance in gene expression patterns, which resulted in detectable levels of specific RNA molecules. The infection of plants with RNA viruses may induce the same control mechanisms at the RNA level. The first mutants defective in PTGS, isolated from Neurospora (qde) [ 36 ] and Arabidopsis (sgs) [ 37 ], will provide us with more information about structural proteins and enzymes involved in PTGS. Finally, the stabilization of transgene expression and targeted knock-out of individual allels of genes, members of gene families or whole gene families are extremely potent applications of PTGS and VIGS in transgene technology and functional genomics.


Gene Regulatory Networks

Eric H. Davidson , Isabelle S. Peter , in Genomic Control Process , 2015

Abstract

Gene regulatory network (GRN) theory defines the principal structural and functional properties of genomic control programs in animals. Here we provide an introductory overview, specifying the components of GRNs, and focusing on higher level design features such as hierarchy, modular organization, and the unidirectionality of these encoded regulatory systems. We consider two major aspects of GRN output, the generation of regulatory states that in turn determine all downstream genetic functions, and the Boolean nature of spatial gene expression that underlies developmental process. The genomic regulatory transactions linked together in GRNs are executed by cis-regulatory modules, and their combinatorial information processing function deeply affect GRN organization. This chapter further includes a first principles quantitative treatment of network dynamics, which rationalizes the measurable kinetics of accumulation of transcriptional products and permits computational assessment of the outputs of regulatory gene cascades. Current GRN theory devolves from multiple earlier roots which we very briefly trace.


Methods

Three approaches for the input sequences

Three approaches were employed for input sequences to discover motifs among multiple sequences [20]. Multiple genes, single species: this is based on the supposition that regulatory motifs are conserved among co-regulated genes within a species, and that the level of gene expression is constant under the chosen experimental conditions. Different transcription factors might have an indirect influence on the same function. Single gene, multiple species: the rate of mutation of a regulatory motif is presumed to be slowed by selective pressure. In a single gene group, therefore, universally conserved regions contain regulatory motifs among cross-species. Conserved regions among closely related species may contain less-functional motifs as noise. On the other hand, alignment can be problematic due to changes in function during evolution across species with large evolutionary distances. Multiple genes, multiple species: alignment of orthologous sequences is used to identify conserved regions these regions are then analyzed as above in Multiple genes and single species. Since potential scores for motif predictions can be improved by alignment of multiple genomes [21], this approach here was adopted to detect regulatory motifs.


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